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#include "config.h"
#include "IOUtil.h"
#include "ContigNode.h"
#include "Uncompress.h"
#include "Graph/ContigGraph.h"
#include "Graph/ContigGraphAlgorithms.h"
#include "Graph/DirectedGraph.h"
#include "Graph/GraphAlgorithms.h"
#include "Graph/GraphIO.h"
#include "Graph/GraphUtil.h"
#include "ContigProperties.h"
#include "SAM.h"
#include <iostream>
#include <sstream>
#include <string>
#include <getopt.h>
#include <boost/tuple/tuple.hpp>
using namespace std;
using namespace boost;
#define PROGRAM "abyss-longseqdist"
static const char VERSION_MESSAGE[] =
PROGRAM " (" PACKAGE_NAME ") " VERSION "\n"
"Written by Anthony Raymond.\n"
"\n"
"Copyright 2014 Canada's Michael Smith Genome Science Centre\n";
static const char USAGE_MESSAGE[] =
"Usage: " PROGRAM " -k<kmer> [OPTION]... SAM >DIST\n"
"Generate distance estimates between all contigs a single\n"
"read maps to.\n"
"\n"
" Arguments:\n"
"\n"
" SAM BWA-MEM alignments of long sequences to the assembly\n"
" DIST estimates of the distance between contigs\n"
"\n"
" Options:\n"
"\n"
" -k, --kmer=N length of a k-mer\n"
" --min-gap=N minimum scaffold gap length to output [200]\n"
" -v, --verbose display verbose output\n"
" --help display this help and exit\n"
" --version output version information and exit\n"
"\n"
"Report bugs to <" PACKAGE_BUGREPORT ">.\n";
namespace opt {
unsigned k; // used by ContigProperties
/** Minimum scaffold gap length to output. */
static int minGap = 200;
/** Verbose output. */
int verbose; // used by PopBubbles
/** Output format */
int format = DOT; // used by DistanceEst
}
static const char shortopts[] = "k:n:o:v";
enum { OPT_HELP = 1, OPT_VERSION, OPT_MIN_GAP };
static const struct option longopts[] = {
{ "kmer", required_argument, NULL, 'k' },
{ "min-gap", required_argument, NULL, OPT_MIN_GAP },
{ "verbose", no_argument, NULL, 'v' },
{ "help", no_argument, NULL, OPT_HELP },
{ "version", no_argument, NULL, OPT_VERSION },
{ NULL, 0, NULL, 0 }
};
/** A distance estimate graph. */
typedef DirectedGraph<Length, DistanceEst> DG;
typedef ContigGraph<DG> Graph;
static void processQuery(vector<Alignment>& recs, Graph& g)
{
typedef graph_traits<Graph>::vertex_descriptor V;
typedef graph_traits<Graph>::edge_descriptor E;
typedef edge_property<Graph>::type EP;
if (recs.size() <= 1)
return;
sort(recs.begin(), recs.end());
for (vector<Alignment>::const_iterator itx = recs.begin();
itx != recs.end(); itx++) {
for (vector<Alignment>::const_iterator ity = itx + 1;
ity != recs.end(); ity++) {
// if aligned to the same contig, don't draw self edge
if (itx->contig == ity->contig)
continue;
// if y is subsumed in x don't draw edge
unsigned xqend = itx->read_start_pos + itx->align_length;
unsigned yqend = ity->read_start_pos + ity->align_length;
if (xqend >= yqend)
continue;
V u = find_vertex(itx->contig, itx->isRC, g);
V v = find_vertex(ity->contig, ity->isRC, g);
E e;
EP ep(opt::minGap, 1, opt::minGap);
bool found;
tie(e, found) = edge(u, v, g);
if (found) {
EP& ep = g[e];
ep.numPairs++;
} else
add_edge(u, v, ep, g);
}
}
}
static void readAlignments(istream& in, Graph& g)
{
SAMRecord rec, prev;
vector<Alignment> recs;
int i = 0;
while (in >> prev && (prev.isUnmapped() || prev.mapq == 0));
recs.push_back(prev);
while (in >> rec) {
if (rec.isUnmapped() || rec.mapq == 0)
continue;
if (opt::verbose > 0 && ++i % 100000 == 0)
cerr << "Processed " << i << " good alignments...\n";
if (rec.qname != prev.qname) {
processQuery(recs, g);
recs.clear();
prev = rec;
recs.push_back(prev);
} else
recs.push_back(rec);
}
if (opt::verbose > 0)
cerr << "Processed " << i << " good alignments.\n";
processQuery(recs, g);
}
int main(int argc, char** argv)
{
bool die = false;
for (int c; (c = getopt_long(argc, argv,
shortopts, longopts, NULL)) != -1;) {
istringstream arg(optarg != NULL ? optarg : "");
switch (c) {
case '?':
die = true;
break;
case 'k':
arg >> opt::k;
break;
case 'v':
opt::verbose++;
break;
case OPT_MIN_GAP:
arg >> opt::minGap;
break;
case OPT_HELP:
cout << USAGE_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_VERSION:
cout << VERSION_MESSAGE;
exit(EXIT_SUCCESS);
}
if (optarg != NULL && !arg.eof()) {
cerr << PROGRAM ": invalid option: `-"
<< (char)c << optarg << "'\n";
exit(EXIT_FAILURE);
}
}
if (opt::k <= 0) {
cerr << PROGRAM ": missing -k,--kmer option\n";
die = true;
}
if (argc - optind != 1) {
cerr << PROGRAM ": incorrect number of arguments\n";
die = true;
}
if (die) {
cerr << "Try `" << PROGRAM
<< " --help' for more information.\n";
exit(EXIT_FAILURE);
}
if (opt::verbose > 0)
cerr << "Reading graph file '" << argv[optind] << "`...\n";
Graph g;
ifstream in(argv[optind]);
in >> g;
g_contigNames.lock();
if (opt::verbose > 0)
cerr << "Finished reading graph.\n";
if (in.eof()) {
cerr << PROGRAM ": there are no alignments\n";
exit(EXIT_FAILURE);
}
if (opt::verbose > 0)
cerr << "Processing alignments from '" << argv[optind] << "`...\n";
readAlignments(in, g);
write_dot(cout, g);
return 0;
}
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